Dev bilayers

[TorecLuik]

This pull request introduces significant enhancements to the biomero schema validation and parsing tool, focusing on improved file format support, expanded schema capabilities, and better test coverage. The most notable changes include support for YAML descriptor files, new computed fields in the schema model, broader parameter options, and a comprehensive test suite for the new features.

File format and CLI improvements:

• Added support for loading and validating YAML descriptor files in addition to JSON, updating CLI argument names and internal logic to handle both formats. [1] [2] [3]

Schema model enhancements:

• Introduced computed fields requires_zarr and requires_plate to WorkflowSchema, which automatically detect if any image input requires ZARR format or has a plate subtype. These fields are included in serialized output. [1] [2]
• Expanded supported types and options for parameters:
  • Added "docker" as a valid container type.
  • Allowed "zarr" and "omezarr" as valid image formats.
  • Extended Parameter and OutputParameter to support new fields: mode, value_choices, value_choices_labels, output_dir_set, and broader types for format and sub_type.

Testing and workflow updates:

• Added a new test suite (tests/test_computed_fields.py) covering computed fields, parameter options, and serialization, ensuring correctness and future maintainability.
• Updated project dependencies and CI:
  • Added pyyaml and pytest dependencies.
  • Enabled tests to run on both Windows and macOS via GitHub Actions, and included a test task in the Pixi configuration. [1] [2] [3]